Luận án Nghiên cứu đặc điểm kháng kháng sinh và gen liên quan ở các chủng salmonella đa kháng

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Biomembr., 2018, 1860(4), 868- 877. 1 PHỤ LỤC Phụ lục 1. Kết quả kiểm tra chất lượng thư viện cDNA bằng máy Bioanalyzer. 2 3 4 Phụ lục 2. Gen độc lực biểu hiện ở các mẫu nghiên cứu. Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG000444 + + + + + + Fimbriae-like adhesin FimI Adherence,Fimbrial VFG000445 + + + + + + Probable fimbrial chaperone SfmC Adherence,Fimbrial VFG000446 + + + + + + Outer membrane usher protein SfmD Adherence,Fimbrial VFG000447 + + + + + + Uncharacterized fimbrial-like protein SfmH Adherence,Fimbrial VFG000448 + + + + + + Uncharacterized fimbrial-like protein SfmF Adherence,Fimbrial VFG000457 + + + + + + Minor curlin subunit CsgB, nucleation component of curlin monomers Adherence,Fimbrial VFG000458 + + + + + + Major curlin subunit precursor CsgA Adherence,Fimbrial VFG000459 + + + + + + Putative curli production protein CsgC Adherence,Fimbrial VFG000460 + + + + + + Curli production assembly/transport component CsgE Adherence,Fimbrial VFG000461 + + + + + + Curli production assembly/transport component CsgF Adherence,Fimbrial VFG000462 + + + + + + Curli production assembly/transport component CsgG Adherence,Fimbrial VFG000464 + + + + + + secreted effector protein Secretion system,Type III secretion system,Invasion VFG000465 + + + + + + Inositol phosphate phosphatase sopB Secretion system,Type III secretion system,Invasion VFG000466 + + + + + + Secreted protein Secretion system,Type III secretion system,Invasion VFG000467 + + + + + + G-nucleotide exchange factor SopE Secretion system,Type III secretion system,Invasion VFG000469 + + + + + + Leucine-rich repeat protein Secretion system,Type III secretion system,Invasion 5 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG000470 + + + + + + SifA protein Secretion system,Type III secretion system VFG000471 + + + + + + Secreted effector J SseJ Secretion system,Type III secretion system VFG000494 + + + + + + Type III secretion protein SsaB Secretion system,Type III secretion system VFG000495 + + + + + + Type III secretion outermembrane pore forming protein (YscC,MxiD,HrcC, InvG) Secretion system,Type III secretion system VFG000496 + + + + + + Type III secretion protein SsaD Secretion system,Type III secretion system VFG000497 + + + + + + Secretion system effector SsaE Secretion system,Type III secretion system VFG000498 + + + + + + Secretion system effector SseA Secretion system,Type III secretion system VFG000499 + + + + + + Type III secretion effector SseB Secretion system,Type III secretion system VFG000500 + + + + + + Secretion system chaparone SscA VFG000501 + + + + + + Secretion system effector SseC Secretion system,Type III secretion system VFG000502 + + + + + + Secretion system effector SseD Secretion system,Type III secretion system VFG000503 + + + + + + Secretion system effector SseE Secretion system,Type III secretion system VFG000504 + + + + + + Secretion system chaparone SscB VFG000505 + + + + + + Type III secretion effector SseF Secretion system,Type III secretion system 6 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG000506 + + + + + + Type III secretion effector SseG Secretion system,Type III secretion system VFG000507 + + + + + + Type III secretion protein SsaG Secretion system,Type III secretion system VFG000508 + + + + + + Type III secretion protein SsaH Secretion system,Type III secretion system VFG000509 + + + + + + Type III secretion protein SsaI Secretion system,Type III secretion system VFG000510 + + + + + + Type III secretion bridge between inner and outermembrane lipoprotein (YscJ,HrcJ,EscJ, PscJ) Secretion system,Type III secretion system VFG000511 + + + + + + Type III secretion protein SsaK Secretion system,Type III secretion system VFG000512 + + + + + + Type III secretion cytoplasmic protein (YscL) Secretion system,Type III secretion system VFG000513 + + + + + + Type III secretion protein SsaM Secretion system,Type III secretion system VFG000514 + + + + + + Type III secretion inner membrane channel protein (LcrD,HrcV,EscV,SsaV) Secretion system,Type III secretion system VFG000515 + + + + + + Type III secretion cytoplasmic ATP synthase (EC 3.6.3.14, YscN,SpaL,MxiB,HrcN,EscN) Secretion system,Type III secretion system VFG000516 + + + + + + Type III secretion spans bacterial envelope protein (YscO) Secretion system,Type III secretion system VFG000517 + + + + + + Type III secretion protein (YscP) Secretion system,Type III secretion system 7 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG000518 + + + + + + Type III secretion inner membrane protein (YscQ,homologous to flagellar export components) Secretion system,Type III secretion system VFG000519 + + + + + + Type III secretion inner membrane protein (YscR,SpaR,HrcR,EscR,homologous to flagellar export components) Secretion system,Type III secretion system VFG000520 + + + + + + Type III secretion inner membrane protein (YscS,homologous to flagellar export components) Secretion system,Type III secretion system VFG000522 + + + + + + Type III secretion inner membrane protein (YscU,SpaS,EscU,HrcU,SsaU, homologous to flagellar export components) Secretion system,Type III secretion system VFG000532 + + + + + + OrgB protein, associated with InvC ATPase of type III secretion system Secretion system,Type III secretion system,Invasion VFG000533 + + + + + + Type III secretion bridge between inner and outermembrane lipoprotein (YscJ,HrcJ,EscJ, PscJ) Secretion system,Type III secretion system,Invasion VFG000534 + + + + + + Pathogenicity 1 island effector protein Secretion system,Type III secretion system,Invasion VFG000535 + + + + + + MxiH protein; Type III secretion cytoplasmic protein (YscF) Secretion system,Type III secretion system,Invasion VFG000536 + + + + + + MxiG protein; Pathogenicity 1 island effector protein Secretion system,Type III secretion system,Invasion VFG000540 + + + + + + Type III secretion injected virulence protein (YopH,tyrosine phosphatase of FAK and p130cas, prevents phagocytosis) Secretion system,Type III secretion system,Invasion 8 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG000541 + + + + + + Chaperone protein SicP Secretion system,Type III secretion system,Invasion VFG000543 + + + + + + Type III secretion injected virulence protein (YopE) Secretion system,Type III secretion system,Invasion VFG000544 + + + + + + Type III secretion host injection protein (YopB); Cell invasion protein SipD (Salmonella invasion protein D) Secretion system,Type III secretion system,Invasion VFG000545 + + + + + + Type III secretion negative modulator of injection (YopK,YopQ,controls size of translocator pore); Cell invasion protein sipC (Effector protein SipC) Secretion system,Type III secretion system,Invasion VFG000546 + + + + + + Cell invasion protein SipB Secretion system,Type III secretion system,Invasion VFG000547 + + + + + + Chaperone protein SicA (Salmonella invasin chaperone) Secretion system,Type III secretion system,Invasion VFG000548 + + + + + + Type III secretion inner membrane protein (YscU,SpaS,EscU,HrcU,SsaU, homologous to flagellar export components); Surface presentation of antigens protein SpaS Secretion system,Type III secretion system,Invasion VFG000549 + + + + + + Surface presentation of antigens protein SpaR; Type III secretion inner membrane protein (YscT,HrcT,SpaR,EscT,EpaR1,homologous to flagellar export components) Secretion system,Type III secretion system,Invasion VFG000550 + + + + + + Type III secretion inner membrane protein (YscS,homologous to flagellar export Secretion system,Type III secretion system,Invasion 9 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại components); Surface presentation of antigens protein SpaQ VFG000551 + + + + + + Type III secretion inner membrane protein (YscR,SpaR,HrcR,EscR,homologous to flagellar export components); Surface presentation of antigens protein SpaP Secretion system,Type III secretion system,Invasion VFG000552 + + + + + + Type III secretion inner membrane protein (YscQ,homologous to flagellar export components); Surface presentation of antigens protein SpaO Secretion system,Type III secretion system,Invasion VFG000553 + + + + + + Type III secretion host injection and negative regulator protein (YopD); Surface presentation of antigens protein SpaN (Invasion protein InvJ) Secretion system,Type III secretion system,Invasion VFG000554 + + + + + + Surface presentation of antigens protein SpaM Secretion system,Type III secretion system,Invasion VFG000555 + + + + + + Type III secretion cytoplasmic ATP synthase (EC 3.6.3.14, YscN,SpaL,MxiB,HrcN,EscN); Probable ATP synthase SpaL (Invasion protein InvC) Secretion system,Type III secretion system,Invasion VFG000556 + + + + + + Type III secretion system protein BsaR; Surface presentation of antigens protein SpaK (Invasion protein InvB) Secretion system,Type III secretion system,Invasion VFG000557 + + + + + + Type III secretion inner membrane channel protein (LcrD,HrcV,EscV,SsaV); Invasion protein InvA Secretion system,Type III secretion system,Invasion 10 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG000558 + + + + + + Type III secretion outermembrane contact sensing protein (YopN,Yop4b,LcrE); Invasion protein InvE Secretion system,Type III secretion system,Invasion VFG000559 + + + + + + Type III secretion outermembrane pore forming protein (YscC,MxiD,HrcC, InvG); Protein InvG precursor Secretion system,Type III secretion system,Invasion VFG000560 + + + + + + Type III secretion thermoregulatory protein (LcrF,VirF,transcription regulation of virulence plasmid) Secretion system,Type III secretion system,Invasion VFG000561 + + + + + + Invasion protein invH precursor Secretion system,Type III secretion system,Invasion VFG000574 + + + + + + Mg(2+) transport ATPase, P-type (EC 3.6.3.2) Magnesium uptake VFG000575 + + + + + + Mg(2+)-transport-ATPase-associated protein MgtC Magnesium uptake VFG000589 + + + + + + Pentapeptide repeat family protein VFG000925 + + + + + + Ferric enterobactin transport ATP-binding protein FepC Iron uptake,Siderophore VFG000926 + + + + + + Ferric enterobactin transport system permease protein FepD Iron uptake,Siderophore VFG000928 + + + + + + Ferric enterobactin transport system permease protein FepG Iron uptake,Siderophore VFG000931 + + + + + + Isochorismate synthase) [enterobactin] siderophore @ Isochorismate synthase of siderophore biosynthesis Iron uptake,Siderophore 11 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG000933 + + + + + + Isochorismatase [enterobactin] siderophore / Apo-aryl carrier domain of EntB @ Isochorismatase of siderophore biosynthesis Iron uptake,Siderophore VFG000934 + + + + + + 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase [enterobactin] siderophore @ 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC 1.3.1.28) of siderophore biosynthesis Iron uptake,Siderophore VFG000935 + + + + + + Outer Membrane Siderophore Receptor IroN Iron uptake,Siderophore receptor VFG001443 + + + + + + Outer membrane protein A precursor Invasion,Serum resistance VFG002302 + + + + + + Transcriptional regulator Resistance to antimicrobial peptides VFG002304 + + + + + + autotransporter Adherence,Nonfimbrial,Au totransporter VFG002305 + + + + + + AIDA autotransporter-like protein Adherence,Nonfimbrial,Au totransporter VFG002306 + + + + + + Putative outer membrane protein Adherence,Nonfimbrial VFG002307 + + + + + + adherence and invasion outermembrane protein (Inv,enhances Peyer's patches colonization) Adherence,Nonfimbrial VFG002319 + + + + + + RNA polymerase sigma factor for flagellar operon Secretion system,Invasion,Motility VFG002329 + + + + + + Flagellar motor switch protein FliG Secretion system,Invasion,Motility VFG002335 + + + + + + Flagellar motor switch protein FliM Secretion system,Invasion,Motility 12 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG002338 + + + + + + Flagellar biosynthesis protein FliP Secretion system,Invasion,Motility VFG002345 + + + + + + Flagellar L-ring protein FlgH Secretion system,Invasion,Motility VFG002346 + + + + + + Flagellar basal-body rod protein FlgG Secretion system,Invasion,Motility VFG002350 + + + + + + Flagellar basal-body rod protein FlgC Secretion system,Invasion,Motility VFG003635 + + + + + + Putative effector protein OrgC of SPI-1 type III secretion system unknown VFG003645 + + + + + + Oxygen-regulated invasion protein OrgA unknown VFG003977 + + + + + + Deubiquitinating protease ElaD unknown VFG003988 + + + + + + secreted effector protein unknown VFG004125 + + + + + + Transcriptional regulator CsgD for 2nd curli operon unknown VFG012513 + + + + + + Glycosyltransferase IroB unknown VFG013418 + + + + + + D-sedoheptulose 7-phosphate isomerase (EC 5.3.1.28) unknown VFG013465 + + + + + + 2-Keto-3-deoxy-D-manno-octulosonate-8- phosphate synthase (EC 2.5.1.55) unknown VFG042066 + + + + + + Putative inner membrane protein unknown VFG042067 + + + + + + hypothetical protein unknown VFG043206 + + + + + + Chemotaxis regulator - transmits chemoreceptor signals to flagellar motor components CheY unknown VFG043210 + + + + + + Positive regulator of CheA protein activity (CheW) unknown 13 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG043213 + + + + + + Flagellar motor rotation protein MotA unknown VFG044165 + + + + + + Enterobactin exporter EntS unknown VFG000521 + + - - + + Type III secretion inner membrane protein (YscT,HrcT,SpaR,EscT,EpaR1,homologous to flagellar export components) Secretion system,Type III secretion system VFG000670 + + + + + + Bactoprenol glucosyl transferase Endotoxin VFG000932 + - + + + + 2,3-dihydroxybenzoate-AMP ligase (EC 2.7.7.58) [enterobactin] siderophore @ 2,3- dihydroxybenzoate-AMP ligase (EC 2.7.7.58) of siderophore biosynthesis Iron uptake,Siderophore VFG002321 + - + - - - Flagellin FliC Secretion system,Invasion,Motility VFG003982 + + - + + + hypothetical protein unknown VFG003997 + + - + + + hypothetical protein unknown VFG020318 + - + - - - Cytolethal distending toxin subunit B, DNase I-like Toxin,Intracellular toxin,DNaseI VFG042068 + + - + + + hypothetical protein unknown VFG000468 - + - + + + - unknown VFG000529 - + + + + + - unknown VFG000669 - + - - - - - unknown VFG004016 - + + + + + - unknown VFG042216 - + + - - - - unknown VFG042552 - - + - - - - unknown VFG042553 - - + - - - - unknown VFG042559 - - + - - - - unknown VFG043209 - - + + + + - unknown VFG000452 - - - + + + - Adherence,Fimbrial 14 Source ID Sal 4 Sal 6 Sal 7 Sal 8 Sal 11 Sal 12 Chức năng Phân loại VFG000453 - - - + + + - Adherence,Fimbrial VFG000454 - - - + + + - Adherence,Fimbrial VFG000455 - - - + + + - Adherence,Fimbrial VFG000456 - - - + + + - Adherence,Fimbrial VFG000463 - - - + + + - Stress protein VFG003971 - - - + + + - unknown VFG004006 - - - - + + - unknown Chú thích: +(gen có biểu hiện), -(gen không biểu hiện), Sal 4 (S. Indiana), Sal 6 (S. Derby), Sal 7 (S. Give), Sal 8 (S. Typhimurium S360), Sal 11 (S. Typhimurium S384), Sal 12 (S. Typhimurium S181). Phụ lục 3. Biểu hiện của các gen liên quan đến flagellar Tên gen Phân loại Chức năng protein flgA Flagellar Flagella basal body P-ring formation protein flgA flgB Flagellar Flagellar basal-body rod protein flgB flgC Flagellar Flagellar basal-body rod protein flgC flgE Flagellar Flagellar hook protein flgE flgF Flagellar Flagellar basal-body rod protein flgF flgG Flagellar Flagellar basal-body rod protein flgG flgH Flagellar Flagellar L-ring protein flgI Flagellar Flagellar P-ring protein flgK Flagellar Flagellar hook-associated protein 1 flgL Flagellar Flagellar hook-associated protein 3 flgN Flagellar Flagella synthesis protein flgN flhA Flagellar Flagellar biosynthesis protein flhA 15 Tên gen Phân loại Chức năng protein flhB Flagellar Flagellar biosynthetic protein flhB flhC Flagellar Flagellar transcriptional regulator FlhC flhD Flagellar Flagellar transcriptional regulator FlhD flhE Flagellar Flagellar protein flhE fliC Flagellar Flagellin fliD Flagellar Flagellar hook-associated protein 2 fliE Flagellar Flagellar hook-basal body complex protein FliE fliF Flagellar Flagellar M-ring protein fliG Flagellar Flagellar motor switch protein FliG fliH Flagellar Flagellar assembly protein fliH fliI Flagellar Flagellum-specific ATP synthase fliJ Flagellar Flagellar fliJ protein fliK Flagellar Flagellar hook-length control protein fliL Flagellar Flagellar protein FliL fliM Flagellar Flagellar motor switch protein FliM fliN Flagellar Flagellar motor switch protein FliN fliO Flagellar Flagellar protein fliO fliP Flagellar Flagellar biosynthetic protein fliP fliQ Flagellar Flagellar biosynthetic protein FliQ fliR Flagellar Flagellar biosynthetic protein fliR fliS Flagellar Flagellar protein fliS fliT Flagellar Flagellar protein FliT flk Flagellar Flagellar regulator flk ycgR Flagellar Flagellar brake protein YcgR motA Flagellar Motility protein A motB Flagellar Motility protein B 16 Phụ lục 4. Các gen tổng hợp LPS và thành tế bào Phân loại Chức năng protein 12 11 8 7 6 4 Capsular and extracellular polysacchrides dTDP-4-dehydrorhamnose reductase + + + + + + Capsular and extracellular polysacchrides Glucose-1-phosphate cytidylyltransferase + + + - + + Capsular and extracellular polysacchrides dTDP-glucose 4,6-dehydratase + + + + + + Capsular and extracellular polysacchrides dTDP-4-dehydrorhamnose 3,5-epimerase + + + + + + Capsular and extracellular polysacchrides Glucose-1-phosphate thymidylyltransferase + + + + + + Capsular and extracellular polysacchrides Putative capsular polysaccharide transport protein YegH + + + - + + Capsular and extracellular polysacchrides O-antigen flippase Wzx + + + - + + Capsular and extracellular polysacchrides Oligosaccharide repeat unit polymerase Wzy + + + - + + Capsular and extracellular polysacchrides UDP-glucose 4-epimerase + + + + + + Capsular and extracellular polysacchrides N-acetylneuraminate lyase + + + + - + Capsular and extracellular polysacchrides Glucosamine-1-phosphate N-acetyltransferase + + + + + + Capsular and extracellular polysacchrides Transcriptional regulator NanR + + + + - + Capsular and extracellular polysacchrides Sialic acid transporter (permease) NanT + + + + - + Capsular and extracellular polysacchrides Glucosamine-6-phosphate deaminase + + + + - + Capsular and extracellular polysacchrides Predicted sialic acid transporter + + + + - + Capsular and extracellular polysacchrides UDP-N-acetylglucosamine 2-epimerase + + + + - + Capsular and extracellular polysacchrides Putative sugar isomerase involved in processing of exogenous sialic acid + + + + - + Capsular and extracellular polysacchrides N-acetylmannosamine kinase + + + + - + Capsular and extracellular polysacchrides N-acetylmannosamine-6-phosphate 2-epimerase + + + + - + Capsular and extracellular polysacchrides N-acetylneuraminic acid outer membrane channel protein NanC + + + + - + Capsular and extracellular polysacchrides Phosphoglucosamine mutase + + + + + + Capsular and extracellular polysacchrides N-acetylglucosamine-1-phosphate uridyltransferase + + + + + + Capsular and extracellular polysacchrides N-acetylglucosamine-6-phosphate deacetylase + + + + - + Capsular and extracellular polysacchrides CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3- sialyltransferase - - - + - + 17 Phân loại Chức năng protein 12 11 8 7 6 4 Capsular and extracellular polysacchrides Sialic acid utilization regulator, RpiR family + + + + - + Gram-Negative cell wall components UDP-glucuronic acid oxidase (UDP-4-keto-hexauronic acid decarboxylating) + + + + + + Gram-Negative cell wall components UDP-4-amino-4-deoxy-L-arabinose formyltransferase + + + + + + Gram-Negative cell wall components Polymyxin resistance protein PmrG + + + + + + Gram-Negative cell wall components UDP-glucose 6-dehydrogenase + + + + + + Gram-Negative cell wall components Protein of unknown function YceH + + + + + + Gram-Negative cell wall components Virulence factor MviM + + + + + + Gram-Negative cell wall components Proposed peptidoglycan lipid II flippase MurJ + + + + + + Gram-Negative cell wall components Protein YhjJ, putative peptidase + + + + + + Gram-Negative cell wall components LysR family transcriptional regulator YhjC + + + + + + Gram-Negative cell wall components Inner membrane protein YhjD + + + + + + Gram-Negative cell wall components Uncharacterized protein YhjG + + + + + + Gram-Negative cell wall components Lipoprotein releasing system transmembrane protein LolC + + + + + + Gram-Negative cell wall components Lipoprotein releasing system transmembrane protein LolE + + + + + + Gram-Negative cell wall components Outer membrane lipoprotein carrier protein LolA + + + + + + Cell Wall and Capsule - no subcategory N-acetylmuramoyl-L-alanine amidase + + + + + + Cell Wall and Capsule - no subcategory D-alanyl-D-alanine carboxypeptidase + + + + + + Cell Wall and Capsule - no subcategory Soluble lytic murein transglycosylase precursor + + + + + + Cell Wall and Capsule - no subcategory Muramoyltetrapeptide carboxypeptidase + + + + + + Cell Wall and Capsule - no subcategory UDP-N-acetylglucosamine 1-carboxyvinyltransferase + + + + + + Cell Wall and Capsule - no subcategory L,D-transpeptidase YcfS + + + + + + Cell Wall and Capsule - no subcategory L,D-transpeptidase YnhG + + + + + + Cell Wall and Capsule - no subcategory L,D-transpeptidase YcbB + + + + + + Cell Wall and Capsule - no subcategory L,D-transpeptidase YbiS + + + + + + Cell Wall and Capsule - no subcategory L,D-transpeptidase ErfK + + + + + + 18 Phân loại Chức năng protein 12 11 8 7 6 4 Cell Wall and Capsule - no subcategory UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso- diaminopimelate ligase + + + + + + Cell Wall and Capsule - no subcategory Gamma-D-Glutamyl-meso-Diaminopimelate Amidase + + + + + + Cell Wall and Capsule - no subcategory AmpG permease + + + + + + Cell Wall and Capsule - no subcategory Membrane-bound lytic murein transglycosylase D precursor - - + - - - Chú thích: +(gen có biểu hiện), -(gen không biểu hiện) 12 (Sal 12), 11 (Sal 11), 8 (Sal 8), 7 (Sal 7), 6 (Sal 6), 4 (Sal 4). Phụ lục 5. Các gen liên quan đến các yếu tố di truyền vận động, phage, và prophage. Tên gen Phân loại Chức năng các gen Sal 12 Sal 11 Sal 8 Sal 7 Sal 6 Sal 4 - Phage tail proteins Phage tail tube protein + + - + + - - Phage tail proteins Phage tail assembly protein I + + + - - - - Phage tail proteins Phage tail/DNA circulation protein + + - + + - - Phage tail proteins Phage tail length tape-measure protein 1 + + + - - - - Phage tail proteins Phage minor tail protein + + + - - + - Phage tail proteins Phage tail length tape-measure protein + + + + + - Phage tail proteins Phage tail assembly protein + + + - - - - Phage replication DNA polymerase III alpha subunit + + + - + + - Phage replication Phage replication protein + + + - + + - Phage packaging machinery Phage terminase, small subunit + + - + + - - Phage packaging machinery Phage terminase, ATPase subunit + + - + + - - Phage packaging machinery Phage terminase, large subunit + + - + + + - Phage packaging machinery Phage portal protein + + + + + + - Phage packaging machinery Phage DNA-binding protein + + - + + - - Phage tail proteins 2 Phage tail assembly protein I + + + - - - - Phage tail proteins 2 Phage tail length tape-measure protein 1 + + + - - - 19 Tên gen Phân loại Chức năng các gen Sal 12 Sal 11 Sal 8 Sal 7 Sal 6 Sal 4 - Phage tail proteins 2 Phage minor tail protein + + + - - + - Phage tail proteins 2 Phage tail length tape-measure protein + + + + + - - Phage tail proteins 2 Phage tail assembly protein + + + - - - - Phage tail fiber proteins Phage tail fiber protein + + + + + + - Phage tail fiber proteins Phage tail fibers + + + + + - - Phage tail fiber proteins Phage tail fiber assembly protein + + + + - - Phage capsid proteins Phage capsid and scaffold + + - + - - - Phage capsid proteins Phage major capsid protein + + + + + + - IbrA and IbrB: co-activators of prophage gene expression Co-activator of prophage gene expression IbrB + + + + + + - IbrA and IbrB: co-activators of prophage gene expression Co-activator of prophage gene expression IbrA + + + + + + - Integrons Integron integrase IntI4 - - + + - - - Integrons Integron integrase IntI1 - - + + - + - Phage tail proteins Phage tail protein - - + + - - - Phage tail proteins Phage tail assembly protein - - + - - - - Phage packaging machinery Phage-related capsid packaging protein - - + - - - - Phage packaging machinery Phage terminase, endonuclease subunit - - + + + + - Phage capsid proteins Phage capsid scaffolding protein - - - + + - - Phage lysis modules Phage endolysin - - - + + - - Phage lysis modules Phage holin - - - + + - - Phage capsid proteins Phage head completion-stabilization protein - - - - + - - Phage lysis modules Phage outer membrane lipoprotein Rz1 - - - - + - - Phage lysis modules Phage spanin Rz - - - - + - - Phage tail proteins Phage tail completion protein - - + - - - - Phage packaging machinery Phage terminase - - + - - - 20 Chú thích: + (gen có biểu hiện), - (gen không biểu hiện), Sal 4 (S. Indiana), Sal 6 (S. Derby), Sal 7 (S. Give), Sal 8 (S. Typhimurium S360), Sal 11 (S. Typhimurium S384), Sal 12 (S. Typhimurium S181). Phụ lục 6. Các gen liên quan đến tác động bất lợi của môi trường biểu hiện ở cả 6 mẫu nghiên cứu. Phân loại Subsystem Chức năng Osmotic stress Osmoregulation Outer membrane protein A precursor Osmotic stress Osmoregulation Propanediol diffusion facilitator Osmotic stress Osmoregulation Osmotically inducible protein OsmY Osmotic stress Osmoregulation Glycerol uptake facilitator protein Osmotic stress Osmoprotectant ABC transporter YehZYXW of Enterobacteriales Osmoprotectant ABC transporter permease protein YehY Osmotic stress Osmoprotectant ABC transporter YehZYXW of Enterobacteriales Osmoprotectant ABC transporter inner membrane protein YehW Osmotic stress Osmoprotectant ABC transporter YehZYXW of Enterobacteriales Osmoprotectant ABC transporter binding protein YehZ Osmotic stress Osmoprotectant ABC transporter YehZYXW of Enterobacteriales Osmoprotectant ABC transporter ATP-binding subunit YehX Osmotic stress Synthesis of osmoregulated periplasmic glucans Glucans biosynthesis protein C (EC 2.1.-.-) Osmotic stress Synthesis of osmoregulated periplasmic glucans Glucans biosynthesis protein D precursor Osmotic stress Synthesis of osmoregulated periplasmic glucans Glucans biosynthesis glucosyltransferase H (EC 2.4.1.-) Osmotic stress Synthesis of osmoregulated periplasmic glucans Glucans biosynthesis protein G precursor Oxidative stress Protection from Reactive Oxygen Species Superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) Oxidative stress Protection from Reactive Oxygen Species Cytochrome c551 peroxidase (EC 1.11.1.5) Oxidative stress Protection from Reactive Oxygen Species Superoxide dismutase [Fe] (EC 1.15.1.1) Oxidative stress Oxidative stress Redox-sensitive transcriptional activator SoxR Oxidative stress Oxidative stress Alkyl hydroperoxide reductase subunit C-like protein Oxidative stress Oxidative stress Superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) 21 Phân loại Subsystem Chức năng Oxidative stress Oxidative stress Paraquat-inducible protein B Oxidative stress Oxidative stress Superoxide dismutase [Fe] (EC 1.15.1.1) Oxidative stress Oxidative stress Ferric uptake regulation protein FUR Oxidative stress Oxidative stress Superoxide dismutase [Mn] (EC 1.15.1.1) Oxidative stress Oxidative stress Nitrite-sensitive transcriptional repressor NsrR Oxidative stress Oxidative stress Paraquat-inducible protein A Oxidative stress Oxidative stress Fumarate and nitrate reduction regulatory protein Oxidative stress Glutathione: Biosynthesis and gamma-glutamyl cycle Gamma-glutamyltranspeptidase (EC 2.3.2.2) Oxidative stress Glutathione: Biosynthesis and gamma-glutamyl cycle Glutathione synthetase (EC 6.3.2.3) Oxidative stress Glutathione: Biosynthesis and gamma-glutamyl cycle Glutamate--cysteine ligase (EC 6.3.2.2) Oxidative stress Glutathione: Non-redox reactions Glutathione S-transferase, zeta (EC 2.5.1.18) Oxidative stress Glutathione: Non-redox reactions Glutathione S-transferase (EC 2.5.1.18) Oxidative stress Glutathione: Non-redox reactions Uncharacterized glutathione S-transferase-like protein Oxidative stress Glutathione: Non-redox reactions Lactoylglutathione lyase (EC 4.4.1.5) Oxidative stress Glutathione: Non-redox reactions FIG005121: SAM-dependent methyltransferase (EC 2.1.1.-) Oxidative stress Glutathione: Non-redox reactions Glutathione S-transferase, omega (EC 2.5.1.18) Oxidative stress Glutathione: Non-redox reactions Uncharacterized GST-like protein yghU associated with glutathionylspermidine synthetase/amidase Oxidative stress Glutathione: Non-redox reactions Hydroxyacylglutathione hydrolase (EC 3.1.2.6) Oxidative stress Glutathione: Non-redox reactions Probable glutathione S-transferase (EC 2.5.1.18), YfcF homolog Oxidative stress Glutathione: Non-redox reactions Probable glutathione S-transferase (EC 2.5.1.18), YfcG homolog Oxidative stress Glutathione: Redox cycle Glutathione reductase (EC 1.8.1.7) Oxidative stress Glutathione: Redox cycle Glutaredoxin-like protein NrdH, required for reduction of Ribonucleotide reductase class Ib 22 Phân loại Subsystem Chức năng Oxidative stress Glutathione: Redox cycle Glutathione peroxidase (EC 1.11.1.9) Oxidative stress Glutathione: Redox cycle Glutaredoxin 3 (Grx3) Oxidative stress Glutathione: Redox cycle Glutaredoxin 1 Oxidative stress Glutathione: Redox cycle Glutaredoxin 2 Oxidative stress Glutaredoxins Glutaredoxin-like protein NrdH, required for reduction of Ribonucleotide reductase class Ib Oxidative stress Glutaredoxins Glutaredoxin 3 (Grx3) Oxidative stress Glutaredoxins Glutaredoxin 1 Oxidative stress Glutaredoxins Glutaredoxin 2 Oxidative stress* Glutaredoxins* Cell wall endopeptidase, family M23/M37* Oxidative stress Glutathionylspermidine and Trypanothione Glutathionylspermidine amidohydrolase (EC 3.5.1.78) Oxidative stress Glutathionylspermidine and Trypanothione Uncharacterized GST-like protein yghU associated with glutathionylspermidine synthetase/amidase Oxidative stress Glutathionylspermidine and Trypanothione Glutathionylspermidine synthase (EC 6.3.1.8) Detoxification Uptake of selenate and selenite Sulfate and thiosulfate import ATP-binding protein CysA (EC 3.6.3.25) Detoxification Uptake of selenate and selenite DedA protein Detoxification Tellurite resistance: Chromosomal determinants Uncharacterized membrane lipoprotein clustered with tellurite resistance proteins TehA/TehB Detoxification Tellurite resistance: Chromosomal determinants FIG005189: putative transferase clustered with tellurite resistance proteins TehA/TehB Detoxification Tellurite resistance: Chromosomal determinants Tellurite resistance protein TehA Detoxification Glutathione-dependent pathway of formaldehyde detoxification S-formylglutathione hydrolase (EC 3.1.2.12) Detoxification Glutathione-dependent pathway of formaldehyde detoxification S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) 23 Phân loại Subsystem Chức năng Periplasmic Stress Periplasmic Stress Response Sigma factor RpoE negative regulatory protein RseA Periplasmic Stress Periplasmic Stress Response Outer membrane stress sensor protease DegS Periplasmic Stress Periplasmic Stress Response Outer membrane protein H precursor Periplasmic Stress Periplasmic Stress Response Intramembrane protease RasP/YluC, implicated in cell division based on FtsL cleavage Periplasmic Stress Periplasmic Stress Response Sigma factor RpoE negative regulatory protein RseB precursor Periplasmic Stress Periplasmic Stress Response Outer membrane stress sensor protease DegQ, serine protease Periplasmic Stress Periplasmic Stress Response HtrA protease/chaperone protein Ghi chú: * Gen không biểu hiện ở Sal 6.